In photosynthesis, a blue/green substance called chlorophyll A and a yellow/green substance called chlorophyll B use light energy (normally sunlight but sometimes artificial) to change carbon dioxide and water into sugars (carbohydrates) and oxygen in the green parts of the plant. The amount of photosynthesis per day which takes place is limited by the duration and intensity of sunlight, and the ability of the green parts of a plant to capture it. The amount of carbon dioxide available can also be a limiting factor. Shortage of water, low temperatures, and leaf disease or damage can reduce photosynthesis, as can shading by other plants, e.g. by weeds in a crop. The cells that contain chlorophyll also have orange/yellow pigments such as xanthophyll and carotene, and brown pigments called pheophytins which absorb different wavelengths of light than the chlorophylls. Crop plants can only build up chlorophyll A and B in the light, and so any leaves that develop in the dark are yellow and cannot efficiently produce carbohydrates. The yellowing of leaves (chlorosis) can also be caused by disease attack, nutrient deficiency or natural senescence (dying off).Chloro- phylls a and b (Chl a, Chl b) represent the majority of the antenna complex pigments and thus are of great im- portance for light absorption, oxygen evolution, and conversion of light energy to chemical energy. In fact, the amount of solar radiation that is absorbed by a leaf is closely related to its chlorophyll concentration (Huang et al. 2014; Gitelson et al. 2014; Samet and Sinclair 1980), which generally is positively related with photosynthetic rate.
Generally, plants modulate leaf anatomy and physiology to irradiance, developing thicker leaves with a greater mesophyll to surface-area ratio (Boardman 1977; Lichtenthaler et al. 1981; Anderson 1986). Common adjustments to high irradiance also include a reduction in the total Chl per unit leaf area and an increased Chl a/b ratio (Bjorkman 1972; Boardman 1977; Lichtenthaler et al. 1981; Anderson 1986). Due to its pre- dictable response to irradiance, the Chl a/b ratio has been proposed as a bioassay to assess the light environment of a plant (Dale and Causton 1992). Under crop production conditions, the irradiance of most leaves is influenced by plant den- sity and row distance and modulates various aspects of the photosynthetic apparatus. Thus, genotype specific Chl composition and content characteristics could have implications for crop management.
The main objectives of this project were to assess genotypic variation in soybean Chl composition and to use genome-wide association mapping to identify genomic loci associated with extract-based measurements of chlorophyll a, chlorophyll b, and total chlorophyll content, as well as chlorophyll a/b ratio.
Chlorophyll contents were determined using extract- and canopy reflectance-based methods. The chlorophyll contents determined from extracts of leaf disks are here- after referred to as chlorophyll a (Chl A), chlorophyll b (Chl B), chlorophyll a/b ratio (Chl Ratio) and total chlorophyll (Chl Total). Briefly, at 54 days after planting (DAP; 2009) and 60 DAP (2010), five 0.68 cm2 leaf disks were collec- ted from the upper-most fully expanded, sun-exposed leaf (3rd or 4th leaf from the stem apex) from five differ- ent plants at flowering (R1-R2 stage). The leaf disks were immediately placed in opaque glass vials containing 5 mL of ethanol (95 %, v/v). Samples were incubated at room temperature in the dark for 24 h, after which, the vials were vigorously agitated. A 200 \(\mu L\) aliquot of each sample was transferred to a 96 well-plate (Costech Analytical Technologies Inc., CA USA) and absorbance measured at 664, 648, and 470 nm on a Scanning Monochromatic Spectrophotometer (Bio-Tek Power- Wave X 340 Microplate Reader, BioTek U.S. VT, USA). Total chlorophyll (Chl Total), chlorophyll a (Chl A), and chlorophyll b (Chl B) were calculated according to Lichtenthaler, expressed on a leaf-area basis (\(\mu g\) \(cm^2\)). The ratio of Chl A and Chl B was determined and is referred to as Chl Ratio.
| Data analysis | Acronym | References |
|---|---|---|
| Extraction and spectrophotometric measurements | ||
| Chlorophyll a | ChlA | Lichtenthaler 1987 |
| Chlorophyll b | ChlB | Lichtenthaler 1987 |
| Chlorophyll a/b ratio | Chl A Chl B ratio | Lichtenthaler 1987 |
| Total chlorophyll | ChlAB Total | Lichtenthaler 1987 |
In this project we applied FARMCPU (Liu et al. 2016) method to find the significant SNPs. FarmCPU is a Genome Wide Association Study (GWAS) method (PLoS Genetics, 2016), standing for “Fixed and random model Circulating Probability Unification”. FarmCPU join the advantages of mixed linear model and stepwise regression (fixed effect model) and overcome their disadvantages by using them iteratively. To eliminate the confounding between kinship in a mixed model (MLM) and genes underlying a trait of interest, FarmCPU substitutes kinship with a set of markers associated with the causal genes. The set of the associated markers are fitted as fixed effect in a fixed effect model for testing markers one at a time across genome. To avoid model overfitting for testing markers, the set of associated markers are optimized in a maximum likelihood method in an MLM with variance and covariance structure defined by the associated markers. Both computer simulation and real data analyses demonstrated that FarmCPU has higher power and less false positives than either MLM or stepwise regression. FARMCPU was run by R package GAPITv3 in our project.
The genotypic data for the 818 soybean accessions (version Wm82.a2) was obtained from the application of the SoySNP50K iSelect BeadChip (Song et al. 2013). In total, 42195 polymorphic SNPs with MAF \(\ge\) 0.01 accross 818 genotypes were used for GWAS mapping of ChlA, ChlB, ChlAB Total, ChlA ChlB ratio. Soybase GWAS position and gene anotation were obtained from (https://soybase.org). Soybase Gene Model positions Glyma we used in this analysis is version 2.0.
The distribution of Chl A, Chl B, and Total Chl look normal distributed in the Fig. , the distribution of Chl A Chl B ratio is bi-bellshape distributed. As in the Table , Chl A and Chl B and Total Chl are highly correllated, and there is not much relations Chl ratio with others.
| Name | Total Chl | Chl A | Chl B | Chl ratio |
|---|---|---|---|---|
| Total Chl | 1.0000000 | 0.9886897 | 0.9066737 | -0.2910365 |
| Chl A | 0.9886897 | 1.0000000 | 0.8331543 | -0.1491333 |
| Chl B | 0.9066737 | 0.8331543 | 1.0000000 | -0.6537444 |
| Chl ratio | -0.2910365 | -0.1491333 | -0.6537444 | 1.0000000 |
As results, we obtained that at the \(\alpha = 0.05\) level of significant, there are 25 SNPs with MAF \(\ge\) 0.01 were identified having significant associations with ChlA, ChlB, ChlAB Total levels and ChlA ChlB ratio. There are 14 SNPs (Table ) identified in 9 loci (Table ) associated with ChlA ChlB ratio, 4 SNPs (Table ) identified in 4 loci(Table ) associated with ChlA, 7 SNPs (Table ) identified in 3 loci(Table ) associated with ChlB and 2 SNPs (Table ) indentified in 2 loci(Table ) associated with Total ChlA ChlB. There are 2 SNPs associated to both ChlA ChlB ratio and ChlB, the other pairs have no commond association. We also observe that the results do not change if we choose the significant level to 0.01 (Fig. , , ,).
Figure 2.1: Box plots and histogram for Chls
| SNP | Chromosome | Position | P.value | maf | effect | Variance_Explained | Type |
|---|---|---|---|---|---|---|---|
| ss715579621 | 1 | 47717883 | 0e+00 | 0.1210269 | -0.0327613 | 0.0179808 | Chl A/B ratio |
| ss715580343 | 1 | 53141084 | 0e+00 | 0.3007335 | -0.0807571 | 0.0338340 | Chl A/B ratio |
| ss715580344 | 1 | 53151056 | 0e+00 | 0.2866748 | -0.0246138 | 0.0042362 | Chl A/B ratio |
| ss715580552 | 1 | 55263448 | 2e-07 | 0.0550122 | 0.0329895 | 0.0026452 | Chl A/B ratio |
| ss715590313 | 5 | 4423839 | 0e+00 | 0.3349633 | -0.0559207 | 0.0009964 | Chl A/B ratio |
| ss715590996 | 5 | 34335534 | 0e+00 | 0.3044010 | -0.0299305 | 0.0150065 | Chl A/B ratio |
| ss715602773 | 8 | 8571552 | 0e+00 | 0.2542787 | 0.0201908 | 0.0040270 | Chl A/B ratio |
| ss715602901 | 8 | 9837263 | 0e+00 | 0.1674817 | 0.0661252 | 0.0022085 | Chl A/B ratio |
| ss715599152 | 8 | 10102541 | 0e+00 | 0.2310513 | 0.0016118 | 0.0022100 | Chl A/B ratio |
| ss715610699 | 11 | 4259267 | 0e+00 | 0.3783619 | 0.0181413 | 0.0168382 | Chl A/B ratio |
| ss715610815 | 11 | 5060627 | 0e+00 | 0.3734719 | 0.0254823 | 0.0024868 | Chl A/B ratio |
| ss715609725 | 11 | 13764673 | 1e-07 | 0.0226161 | -0.1407266 | 0.0051594 | Chl A/B ratio |
| ss715609736 | 11 | 14122451 | 0e+00 | 0.0244499 | -0.0622868 | 0.0039476 | Chl A/B ratio |
| ss715610196 | 11 | 31286570 | 0e+00 | 0.0201711 | 0.0347399 | 0.0000000 | Chl A/B ratio |
| ss715581005 | 2 | 11686919 | 0e+00 | 0.2218826 | 1.3176296 | 0.0031495 | Chl A |
| ss715598780 | 7 | 86898 | 0e+00 | 0.0354523 | 0.2716099 | 0.0406689 | Chl A |
| ss715599055 | 7 | 9535961 | 1e-07 | 0.2701711 | 1.3153512 | 0.0000000 | Chl A |
| ss715624377 | 16 | 31172215 | 0e+00 | 0.0152812 | -4.7230635 | 0.1614091 | Chl A |
| ss715580343 | 1 | 53141084 | 0e+00 | 0.3007335 | -0.1594132 | 0.0000000 | Chl B |
| ss715580344 | 1 | 53151056 | 0e+00 | 0.2866748 | -0.6818936 | 0.0147080 | Chl B |
| ss715598601 | 7 | 7349078 | 0e+00 | 0.3306846 | -0.3663648 | 0.0000000 | Chl B |
| ss715598602 | 7 | 7354616 | 0e+00 | 0.3312958 | 0.3977816 | 0.0095525 | Chl B |
| ss715597527 | 7 | 37049207 | 1e-07 | 0.4425428 | 0.0951097 | 0.0083861 | Chl B |
| ss715623433 | 16 | 13285061 | 1e-07 | 0.1185819 | -0.5628720 | 0.0142384 | Chl B |
| ss715627201 | 17 | 37093778 | 0e+00 | 0.1393643 | 0.5833435 | 0.0214669 | Chl B |
| ss715581877 | 2 | 29620600 | 1e-07 | 0.3539120 | 1.5139055 | 0.0029779 | Total Chl A Chl B |
| ss715604090 | 9 | 3931954 | 1e-07 | 0.0525672 | 2.9529925 | 0.1118926 | Total Chl A Chl B |
The Vienn diagram Fig. shows us the relations of significant SNPs among Chl A, Chl B, Chl AB total and Chl A/B ratio.
Figure 2.2: Venn diagram for relations of Chl types
There are (14, 4, 7, 2 ) SNPs that are significant associated (respectively) to ChlA ChlB ratio, ChlA, ChlB and Total Chl. However, there is no significant SNPs that belong to all 4 catergories.
According to Soybase GWAS position dataset obtained from website (https://soybase.org), our results show that there is only one SNP (table ) that is significant explained by the Chlorophyll ratio and there is no SNP that is in Soybase GWAS position dataset associated with Chl A, Total Chl, and Chl B. The following table is the detail of the significant SNPs.
| SNP | Chromosome | Position | P.value | maf | effect | Variance_Explained | Trait |
|---|---|---|---|---|---|---|---|
| ss715590996 | 5 | 34335534 | 0 | 0.304401 | -0.0299305 | 0.0150065 | Chl A Chl B ratio |
| Loci | Feature Name | Start | End | Distance to SNP | Functional annotation |
|---|---|---|---|---|---|
| 1 | Glyma.01g153500 | 49096486 | 49097279 | 1.378603 | Photosynthetic reaction centre protein |
| 2 | Glyma.01g204700 | 53740048 | 53741473 | 0.598964 | Chlorophyll A-B binding protein |
| Glyma.01g226700 | 55505550 | 55515233 | 2.364466 | von Willebrand factor type A domain; Magnesium chelatase, subunit ChlI | |
| 3 | Glyma.05g026200 | 2281768 | 2284008 | 2.139831 | Pyridine nucleotide-disulphide oxidoreductase |
| Glyma.05g066100 | 6479570 | 6481579 | 2.055731 | sequence-specific DNA binding transcription factor activity | |
| 4 | Glyma.05g128000 | 32149719 | 32150849 | 2.184685 | Chlorophyll A-B binding protein |
| Glyma.05g129700 | 32281938 | 32287791 | 2.047743 | MCM2/3/5 family | |
| Glyma.05g149400 | 34365927 | 34369714 | 0.030393 | PRONE (Plant-specific Rop nucleotide exchanger); Chlorophyll A-B binding protein | |
| Glyma.05g156300 | 34881112 | 34887058 | 0.545578 | Pheophorbide a oxygenase; Rieske [2Fe-2S] domain | |
| 5 | Glyma.08g074000 | 5651670 | 5653067 | 2.918485 | Chlorophyll A-B binding protein |
| Glyma.08g082900 | 6276579 | 6277935 | 2.293617 | Chlorophyll A-B binding protein | |
| Glyma.08g084400 | 6360443 | 6366566 | 2.204986 | MCM2/3/5 family | |
| Glyma.08g114300 | 8746643 | 8747874 | 0.175091 | IRON-SULFUR DOMAIN CONTAINING PROTEIN | |
| Glyma.08g114400 | 8750828 | 8756629 | 0.179276 | Pheophorbide a oxygenase; Rieske [2Fe-2S] domain | |
| 7 | Glyma.11g101800 | 7719377 | 7722788 | 2.658750 | GTP-BINDING PROTEIN-RELATED |
| 8 | Glyma.11g149600 | 11642938 | 11645593 | 2.119080 | molecular function |
| 9 | Glyma.11g228800 | 32398995 | 32402927 | 1.112425 | Chlorophyll A-B binding protein |
We found that the following genes Glyma01g41320, Glyma01g43630, Glyma05g01000, Glyma05g05450 in our results were also identified by (Dhanapal et al. 2016).
Among the significant SNPs, there are 4 SNPs ss715580343, ss715580344, ss715598602, ss715604090in exon regions.
| Loci | Feature Name | Start | End | Distance to SNP | Functional annotation |
|---|---|---|---|---|---|
| 1 | Glyma.02g134200 | 13867709 | 13869124 | 2.180790 | alpha/beta hydrolase fold |
| 2 | Glyma.07g000500 | 62458 | 75399 | 0.011499 | NmrA-like family; Complex I intermediate-associated protein 30 (CIA30) |
| Glyma.07g029900 | 2383023 | 2386348 | 2.296125 | molecular function | |
| 3 | Glyma.07g085700 | 7910707 | 7915213 | 1.620748 | short chain dehydrogenase |
| Glyma.07g096800 | 9079793 | 9081431 | 0.454530 | Chlorophyllase | |
| Glyma.07g096900 | 9083837 | 9085839 | 0.450122 | Chlorophyllase | |
| Glyma.07g097000 | 9118318 | 9120182 | 0.415779 | Chlorophyllase | |
| 4 | Glyma.16g132500 | 28902729 | 28905667 | 2.266548 | alpha/beta hydrolase fold |
| Glyma.16g138000 | 29508469 | 29514252 | 1.657963 | alpha/beta hydrolase fold | |
| Glyma.16g145800 | 30677170 | 30679559 | 0.492656 | Chlorophyll A-B binding protein | |
| Glyma.16g162600 | 32154717 | 32155227 | 0.982502 | Chlorophyll A-B binding protein | |
| Glyma.16g165200 | 32442602 | 32444100 | 1.270387 | Chlorophyll A-B binding protein | |
| Glyma.16g165500 | 32457671 | 32458673 | 1.285456 | Chlorophyll A-B binding protein | |
| Glyma.16g165800 | 32484354 | 32486237 | 1.312139 | Chlorophyll A-B binding protein |
| Loci | Feature Name | Start | End | Distance to SNP | Functional annotation |
|---|---|---|---|---|---|
| 1 | Glyma.01g204700 | 53740048 | 53741473 | 0.598964 | Chlorophyll A-B binding protein |
| Glyma.01g226700 | 55505550 | 55515233 | 2.364466 | von Willebrand factor type A domain; Magnesium chelatase, subunit ChlI | |
| 2 | Glyma.07g085700 | 7910707 | 7915213 | 0.561629 | short chain dehydrogenase |
| Glyma.07g096800 | 9079793 | 9081431 | 1.730715 | Chlorophyllase | |
| Glyma.07g096900 | 9083837 | 9085839 | 1.734759 | Chlorophyllase | |
| Glyma.07g097000 | 9118318 | 9120182 | 1.769240 | Chlorophyllase | |
| 3 | Glyma.07g204300 | 37333134 | 37335896 | 0.283927 | Magnesium chelatase, subunit ChlI |
| Glyma.07g211000 | 38220165 | 38221079 | 1.170958 | alpha/beta hydrolase fold |
| Loci | Feature Name | Start | End | Distance to SNP | Functional annotation |
|---|---|---|---|---|---|
| 1 | Glyma.02g170600 | 26652157 | 26657142 | 2.963458 | MCM2/3/5 family |
| 2 | Glyma.09g047300 | 4077473 | 4083792 | 0.145519 | MCM2/3/5 family |
| SNP | Chr | P-value | effect | Var. Explained | MAF | Minor | Adj.FDR | Type |
|---|---|---|---|---|---|---|---|---|
| BARC_1.01_Gm01_46841836_T_C | 1 | 0e+00 | -0.0327613 | 0.0179808 | 0.1210269 | C | 0.0000187 | Chl A/B ratio |
| BARC_1.01_Gm01_46841836_T_C | 1 | 0e+00 | -0.0327613 | 0.0179808 | 0.1210269 | T | 0.0000187 | Chl A/B ratio |
| BARC_1.01_Gm01_52253980_C_T | 1 | 0e+00 | -0.0807571 | 0.0338340 | 0.3007335 | T | 0.0000000 | Chl A/B ratio |
| BARC_1.01_Gm01_52253980_C_T | 1 | 0e+00 | -0.0807571 | 0.0338340 | 0.3007335 | C | 0.0000000 | Chl A/B ratio |
| BARC_1.01_Gm01_52263952_T_C | 1 | 0e+00 | -0.0246138 | 0.0042362 | 0.2866748 | C | 0.0000000 | Chl A/B ratio |
| BARC_1.01_Gm01_52263952_T_C | 1 | 0e+00 | -0.0246138 | 0.0042362 | 0.2866748 | T | 0.0000000 | Chl A/B ratio |
| BARC_1.01_Gm01_54354945_G_A | 1 | 2e-07 | 0.0329895 | 0.0026452 | 0.0550122 | G | 0.0005466 | Chl A/B ratio |
| BARC_1.01_Gm01_54354945_G_A | 1 | 2e-07 | 0.0329895 | 0.0026452 | 0.0550122 | A | 0.0005466 | Chl A/B ratio |
| BARC_1.01_Gm05_2708074_T_C | 5 | 0e+00 | -0.0559207 | 0.0009964 | 0.3349633 | T | 0.0000079 | Chl A/B ratio |
| BARC_1.01_Gm05_34064933_C_T | 5 | 0e+00 | -0.0299305 | 0.0150065 | 0.3044010 | T | 0.0000079 | Chl A/B ratio |
| BARC_1.01_Gm08_8541523_G_T | 8 | 0e+00 | 0.0201908 | 0.0040270 | 0.2542787 | T | 0.0000337 | Chl A/B ratio |
| BARC_1.01_Gm08_8541523_G_T | 8 | 0e+00 | 0.0201908 | 0.0040270 | 0.2542787 | G | 0.0000337 | Chl A/B ratio |
| BARC_1.01_Gm08_9845186_T_C | 8 | 0e+00 | 0.0661252 | 0.0022085 | 0.1674817 | C | 0.0000275 | Chl A/B ratio |
| BARC_1.01_Gm08_9845186_T_C | 8 | 0e+00 | 0.0661252 | 0.0022085 | 0.1674817 | T | 0.0000275 | Chl A/B ratio |
| BARC_1.01_Gm08_10189778_C_T | 8 | 0e+00 | 0.0016118 | 0.0022100 | 0.2310513 | T | 0.0001441 | Chl A/B ratio |
| BARC_1.01_Gm08_10189778_C_T | 8 | 0e+00 | 0.0016118 | 0.0022100 | 0.2310513 | C | 0.0001441 | Chl A/B ratio |
| BARC_1.01_Gm11_4249856_G_A | 11 | 0e+00 | 0.0181413 | 0.0168382 | 0.3783619 | G | 0.0000000 | Chl A/B ratio |
| BARC_1.01_Gm11_4249856_G_A | 11 | 0e+00 | 0.0181413 | 0.0168382 | 0.3783619 | A | 0.0000000 | Chl A/B ratio |
| BARC_1.01_Gm11_5051077_T_G | 11 | 0e+00 | 0.0254823 | 0.0024868 | 0.3734719 | G | 0.0000253 | Chl A/B ratio |
| BARC_1.01_Gm11_5051077_T_G | 11 | 0e+00 | 0.0254823 | 0.0024868 | 0.3734719 | T | 0.0000253 | Chl A/B ratio |
| BARC_1.01_Gm11_24232656_C_T | 11 | 1e-07 | -0.1407266 | 0.0051594 | 0.0226161 | T | 0.0002199 | Chl A/B ratio |
| BARC_1.01_Gm11_24590514_T_C | 11 | 0e+00 | -0.0622868 | 0.0039476 | 0.0244499 | C | 0.0001444 | Chl A/B ratio |
| BARC_1.01_Gm11_24590514_T_C | 11 | 0e+00 | -0.0622868 | 0.0039476 | 0.0244499 | T | 0.0001444 | Chl A/B ratio |
| BARC_1.01_Gm11_35762107_A_G | 11 | 0e+00 | 0.0347399 | 0.0000000 | 0.0201711 | G | 0.0001444 | Chl A/B ratio |
| BARC_1.01_Gm11_35762107_A_G | 11 | 0e+00 | 0.0347399 | 0.0000000 | 0.0201711 | A | 0.0001444 | Chl A/B ratio |
| BARC_1.01_Gm02_32796990_G_A | 2 | 1e-07 | 1.5139055 | 0.0029779 | 0.3539120 | A | 0.0011014 | Total Chl |
| BARC_1.01_Gm09_3889437_T_C | 9 | 1e-07 | 2.9529925 | 0.1118926 | 0.0525672 | C | 0.0011014 | Total Chl |
| BARC_1.01_Gm01_52253980_C_T | 1 | 0e+00 | -0.1594132 | 0.0000000 | 0.3007335 | T | 0.0000805 | Chl B |
| BARC_1.01_Gm01_52253980_C_T | 1 | 0e+00 | -0.1594132 | 0.0000000 | 0.3007335 | C | 0.0000805 | Chl B |
| BARC_1.01_Gm01_52263952_T_C | 1 | 0e+00 | -0.6818936 | 0.0147080 | 0.2866748 | C | 0.0000000 | Chl B |
| BARC_1.01_Gm01_52263952_T_C | 1 | 0e+00 | -0.6818936 | 0.0147080 | 0.2866748 | T | 0.0000000 | Chl B |
| BARC_1.01_Gm07_7309830_T_C | 7 | 0e+00 | -0.3663648 | 0.0000000 | 0.3306846 | T | 0.0000001 | Chl B |
| BARC_1.01_Gm07_7309830_T_C | 7 | 0e+00 | -0.3663648 | 0.0000000 | 0.3306846 | C | 0.0000001 | Chl B |
| BARC_1.01_Gm07_7315368_T_C | 7 | 0e+00 | 0.3977816 | 0.0095525 | 0.3312958 | T | 0.0001274 | Chl B |
| BARC_1.01_Gm07_7315368_T_C | 7 | 0e+00 | 0.3977816 | 0.0095525 | 0.3312958 | C | 0.0001274 | Chl B |
| BARC_1.01_Gm07_37143613_T_C | 7 | 1e-07 | 0.0951097 | 0.0083861 | 0.4425428 | C | 0.0005649 | Chl B |
| BARC_1.01_Gm16_13425509_T_C | 16 | 1e-07 | -0.5628720 | 0.0142384 | 0.1185819 | T | 0.0003426 | Chl B |
| BARC_1.01_Gm16_13425509_T_C | 16 | 1e-07 | -0.5628720 | 0.0142384 | 0.1185819 | C | 0.0003426 | Chl B |
| BARC_1.01_Gm17_37382483_A_G | 17 | 0e+00 | 0.5833435 | 0.0214669 | 0.1393643 | G | 0.0000652 | Chl B |
| BARC_1.01_Gm02_11350199_T_G | 2 | 0e+00 | 1.3176296 | 0.0031495 | 0.2218826 | G | 0.0005785 | Chl A |
| BARC_1.01_Gm07_9498944_A_G | 7 | 1e-07 | 1.3153512 | 0.0000000 | 0.2701711 | A | 0.0012218 | Chl A |
| BARC_1.01_Gm07_9498944_A_G | 7 | 1e-07 | 1.3153512 | 0.0000000 | 0.2701711 | G | 0.0012218 | Chl A |
Figure 3.1: Distribution of SNPs in Chromosomes
Figure 3.2: Significant SNPs and their Chl types with their positions in Chromosomes
Figure 3.3: Manhattan plot for Chl ratio significants
Figure 3.4: Manhattan plot for Chl A significants
Figure 3.5: Manhattan plot for Chl B significants
Figure 3.6: Manhattan plot for Total Chl significants
Anderson, Jan M. 1986. “Photoregulation of the Composition, Function, and Structure of Thylakoid Membranes.” Annual Review of Plant Physiology 37 (1): 93–136.
Bjorkman, O. 1972. “Effect of Light Intensity During Growth of Atriplex Patula on the Capacity of Photosynthetic Reactions, Chloroplast Components and Structure.” Carnegie Institution Year Book 71: 115–35.
Boardman, NK t. 1977. “Comparative Photosynthesis of Sun and Shade Plants.” Annual Review of Plant Physiology 28 (1): 355–77.
Dale, MP, and DR Causton. 1992. “Use of the Chlorophyll a/B Ratio as a Bioassay for the Light Environment of a Plant.” Functional Ecology, 190–96.
Dhanapal, Arun Prabhu, Jeffery D Ray, Shardendu K Singh, Valerio Hoyos-Villegas, James R Smith, Larry C Purcell, and Felix B Fritschi. 2016. “Genome-Wide Association Mapping of Soybean Chlorophyll Traits Based on Canopy Spectral Reflectance and Leaf Extracts.” BMC Plant Biology 16 (1): 174.
Gitelson, Anatoly A, Yi Peng, Timothy J Arkebauer, and James Schepers. 2014. “Relationships Between Gross Primary Production, Green Lai, and Canopy Chlorophyll Content in Maize: Implications for Remote Sensing of Primary Production.” Remote Sensing of Environment 144: 65–72.
Huang, Wen-Dar, Kuan-Hung Lin, Ming-Huang Hsu, Meng-Yuan Huang, Zhi-Wei Yang, Pi-Yu Chao, and Chi-Ming Yang. 2014. “Eliminating Interference by Anthocyanin in Chlorophyll Estimation of Sweet Potato (Ipomoea Batatas L.) Leaves.” Botanical Studies 55 (1): 11.
Lichtenthaler, HK, C Buschmann, M Döll, H-J Fietz, T Bach, U Kozel, D Meier, and U Rahmsdorf. 1981. “Photosynthetic Activity, Chloroplast Ultrastructure, and Leaf Characteristics of High-Light and Low-Light Plants and of Sun and Shade Leaves.” Photosynthesis Research 2 (2): 115–41.
Liu, Xiaolei, Meng Huang, Bin Fan, Edward S Buckler, and Zhiwu Zhang. 2016. “Iterative Usage of Fixed and Random Effect Models for Powerful and Efficient Genome-Wide Association Studies.” PLoS Genetics 12 (2).
Samet, Joyce S, and Thomas R Sinclair. 1980. “Leaf Senescence and Abscisic Acid in Leaves of Field-Grown Soybean.” Plant Physiology 66 (6): 1164–8.
Song, Qijian, David L Hyten, Gaofeng Jia, Charles V Quigley, Edward W Fickus, Randall L Nelson, and Perry B Cregan. 2013. “Development and Evaluation of Soysnp50k, a High-Density Genotyping Array for Soybean.” PloS One 8 (1).